Carga de paquetes

library(tidyverse)
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library(plotly)
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Importación de datos

Descargar datos genómicos: datos

eukaryotes<-read_csv("data/eukaryotes.csv", col_names = T)
## Parsed with column specification:
## cols(
##   `#Organism Name` = col_character(),
##   `Organism Groups` = col_character(),
##   Strain = col_character(),
##   BioSample = col_character(),
##   BioProject = col_character(),
##   Assembly = col_character(),
##   Level = col_character(),
##   `Size(Mb)` = col_double(),
##   `GC%` = col_double(),
##   Replicons = col_character(),
##   WGS = col_character(),
##   Scaffolds = col_double(),
##   CDS = col_double(),
##   `Release Date` = col_datetime(format = ""),
##   `GenBank FTP` = col_character(),
##   `RefSeq FTP` = col_character()
## )

Exploración y limpieza de datos

eukaryotes %>% glimpse()
## Rows: 5,131
## Columns: 16
## $ `#Organism Name`  <chr> "Emiliania huxleyi CCMP1516", "Arabidopsis thaliana…
## $ `Organism Groups` <chr> "Eukaryota;Protists;Other Protists", "Eukaryota;Pla…
## $ Strain            <chr> "CCMP1516", NA, "A17", NA, NA, NA, NA, NA, NA, "B80…
## $ BioSample         <chr> "SAMN02744062", "SAMN03081427", "SAMN02299339", "SA…
## $ BioProject        <chr> "PRJNA77753", "PRJNA10719", "PRJNA10791", "PRJNA198…
## $ Assembly          <chr> "GCA_000372725.1", "GCA_000001735.1", "GCA_00021949…
## $ Level             <chr> "Scaffold", "Chromosome", "Chromosome", "Chromosome…
## $ `Size(Mb)`        <dbl> 167.67600, 119.66800, 412.92400, 978.97200, 823.786…
## $ `GC%`             <dbl> 64.5000, 36.0528, 34.0470, 35.1208, 35.7097, 0.0000…
## $ Replicons         <chr> NA, "chromosome 1:NC_003070.9/CP002684.1; chromosom…
## $ WGS               <chr> "AHAL01", NA, "APNO01", "ACUP02", "AEKE02", "FJWB02…
## $ Scaffolds         <dbl> 7795, 7, 2187, 1191, 3224, 72295, 58, 279439, 598, …
## $ CDS               <dbl> 38554, 48350, 57661, 71525, 36010, 0, 41070, 0, 584…
## $ `Release Date`    <dttm> 2013-04-19, 2001-08-13, 2011-08-12, 2010-01-05, 20…
## $ `GenBank FTP`     <chr> "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/372…
## $ `RefSeq FTP`      <chr> "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/372…

Selección de columnas de interés

eukaryotes %>% select(c("#Organism Name","Organism Groups","Strain","Size(Mb)","GC%","CDS")) -> eukaryotes_subset
  
eukaryotes_subset %>% head()
## # A tibble: 6 x 6
##   `#Organism Name`       `Organism Groups`        Strain  `Size(Mb)` `GC%`   CDS
##   <chr>                  <chr>                    <chr>        <dbl> <dbl> <dbl>
## 1 Emiliania huxleyi CCM… Eukaryota;Protists;Othe… CCMP15…       168.  64.5 38554
## 2 Arabidopsis thaliana   Eukaryota;Plants;Land P… <NA>          120.  36.1 48350
## 3 Medicago truncatula    Eukaryota;Plants;Land P… A17           413.  34.0 57661
## 4 Glycine max            Eukaryota;Plants;Land P… <NA>          979.  35.1 71525
## 5 Solanum lycopersicum   Eukaryota;Plants;Land P… <NA>          824.  35.7 36010
## 6 Hordeum vulgare        Eukaryota;Plants;Land P… <NA>         9789.   0       0

Renombrar columnas

eukaryotes_subset %>% rename(organism="#Organism Name",groups="Organism Groups",genome_size_mb="Size(Mb)",gc_percent="GC%") %>% rename_with(tolower) -> eukaryotes_subset

eukaryotes_subset %>% head()
## # A tibble: 6 x 6
##   organism           groups              strain  genome_size_mb gc_percent   cds
##   <chr>              <chr>               <chr>            <dbl>      <dbl> <dbl>
## 1 Emiliania huxleyi… Eukaryota;Protists… CCMP15…           168.       64.5 38554
## 2 Arabidopsis thali… Eukaryota;Plants;L… <NA>              120.       36.1 48350
## 3 Medicago truncatu… Eukaryota;Plants;L… A17               413.       34.0 57661
## 4 Glycine max        Eukaryota;Plants;L… <NA>              979.       35.1 71525
## 5 Solanum lycopersi… Eukaryota;Plants;L… <NA>              824.       35.7 36010
## 6 Hordeum vulgare    Eukaryota;Plants;L… <NA>             9789.        0       0

Separar columna “groups” en tres: “domain”, “kingdom”, “class”

eukaryotes_subset %>% separate(groups,c("domain","kingdom","class"),sep = ";") -> eukaryotes_subset

eukaryotes_subset %>% head()
## # A tibble: 6 x 8
##   organism       domain  kingdom  class   strain genome_size_mb gc_percent   cds
##   <chr>          <chr>   <chr>    <chr>   <chr>           <dbl>      <dbl> <dbl>
## 1 Emiliania hux… Eukary… Protists Other … CCMP1…           168.       64.5 38554
## 2 Arabidopsis t… Eukary… Plants   Land P… <NA>             120.       36.1 48350
## 3 Medicago trun… Eukary… Plants   Land P… A17              413.       34.0 57661
## 4 Glycine max    Eukary… Plants   Land P… <NA>             979.       35.1 71525
## 5 Solanum lycop… Eukary… Plants   Land P… <NA>             824.       35.7 36010
## 6 Hordeum vulga… Eukary… Plants   Land P… <NA>            9789.        0       0
eukaryotes_subset %>% group_by(kingdom) %>% count()
## # A tibble: 5 x 2
## # Groups:   kingdom [5]
##   kingdom      n
##   <chr>    <int>
## 1 Animals   1250
## 2 Fungi     2844
## 3 Other       20
## 4 Plants     478
## 5 Protists   539
eukaryotes_subset %>% group_by(kingdom) %>% summarise(mean=mean(genome_size_mb),sd=sd(genome_size_mb),max=max(genome_size_mb),min=min(genome_size_mb))
## `summarise()` ungrouping output (override with `.groups` argument)
## # A tibble: 5 x 5
##   kingdom    mean     sd    max    min
##   <chr>     <dbl>  <dbl>  <dbl>  <dbl>
## 1 Animals  1132.  1434.  32394.  0.663
## 2 Fungi      29.9   20.2   216.  2.08 
## 3 Other     108.   129.    543. 12.1  
## 4 Plants   1023.  2738.  27603.  0.986
## 5 Protists   46.7   57.1   808.  1.45
eukaryotes_subset %>% select(organism,kingdom,class,genome_size_mb) %>%  group_by(kingdom) %>% top_n(.,n = 1,wt = genome_size_mb)
## # A tibble: 5 x 4
## # Groups:   kingdom [5]
##   organism                     kingdom  class          genome_size_mb
##   <chr>                        <chr>    <chr>                   <dbl>
## 1 Ambystoma mexicanum          Animals  Amphibians             32394.
## 2 Pinus lambertiana            Plants   Land Plants            27603.
## 3 Saccharina japonica          Other    Other                    543.
## 4 Uromyces viciae-fabae        Fungi    Basidiomycetes           216.
## 5 Symbiodinium microadriaticum Protists Other Protists           808.
eukaryotes_subset %>% ggplot(.,aes(x=kingdom,y=genome_size_mb,color=kingdom)) +
  geom_point(alpha=0.3) + geom_boxplot(alpha=0.5)

eukaryotes_subset %>% filter(genome_size_mb >0 & cds > 0) %>% ggplot(.,aes(x=cds,y=genome_size_mb,color=kingdom, size=cds)) +
  geom_point(alpha=0.5) -> p
p

library(plotly)
library(cowplot)
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## Note: As of version 1.0.0, cowplot does not change the
##   default ggplot2 theme anymore. To recover the previous
##   behavior, execute:
##   theme_set(theme_cowplot())
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options(scipen = 999)
eukaryotes_subset %>% mutate(genome_size_mb=round(genome_size_mb,2)) %>% ggplot(.,aes(x=kingdom,y=genome_size_mb,color=kingdom, alpha=0.4,text= paste("organism:",organism,"\ncds:",cds))) +
  geom_point() +theme_cowplot(12) -> p
ggplotly(p, tooltip = c("text","x","y")) %>% config(displayModeBar = F)